/galaxy/srv/galaxy/server/lib/galaxy/webapps/galaxy/
changed: [galaxy01.educloud.no] => {
"msg": "Galaxy version changed from '' to '60ab1d5b7ae4385ca31307b0c23c52c979e337eb'"
}
failed to download http://cvmfs0-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/data/6b/81f0681da21040ce0b4a31c3602255a19c5032P (9 - host returned HTTP error)
unexpected HTTP error code 200 - please check the stratum 0 healthStill getting this same error when trying to replicate stratum 0 singularity repo. Was it not rebuilt? Or has the stratum 0 URL changed? The data repo is replicating successfully. Thanks for any pointers.
galaxy_systemd_zergling_envand galaxy_zergpool_listen_addr. In the latest version where mule is the only systemd mode, there is only galaxy_systemd_envvariable. I am using it but the DRMAA_LIBRARY_PATH=.... variable which I set there is now missing in the galaxy.service file. Is this correct?
# systemd
galaxy_systemd_mode: mule
__galaxy_systemd_memory_limit_merged:
mule: 32
galaxy_systemd_env: "DRMAA_LIBRARY_PATH=/galaxy/srv/drmaa/lib/libdrmaa.so.1"
#galaxy_zergpool_listen_addr: 127.0.0.1:8080
galaxy_restart_handler_name: "Restart Galaxy"
#galaxy_systemd_zergling_env: "DRMAA_LIBRARY_PATH=/srv/drmaa/lib/libdrmaa.so.1"
Hello all. I've been experimenting with using mamba instead of conda on pulsar and running tool tests (not in parallel) to get environments to install. It has been great and fast but at one point there was an error:
LockError:
LOCKERROR: It looks like conda is already doing something.
The lock ['/mnt/pulsar/deps/_conda/pkgs/cache.pid1069995.conda_lock'] was found. Wait for it to finish before continuing.As far as I could see there were no conda processes running, and as soon as I deleted the lock file things worked again but in the meantime several of my test jobs failed because their environments had not installed. I'm wondering if it's safe to use mamba as the conda exec.
Hi admins, I am trying to update our galaxy at rothamsted from v20.09 to new v21.09.
1) Have taken snapshot of old galaxy + backup of postgresDB and verified we use python 3.6.8 on our galaxy VM's + hpc/slurm here,
2) got the new release_21.09 code/branch from github,
3) reviewed and amended configs: galxy.yml (added our logging setup), job_conf.xml (for our Slurm setup, auth_conf.xml (for python-pam, our institute AD login), tool_conf.xml, datatypes_conf.xml, etc.,
4) also updated python-pam, drmaa, daemonize in our galaxy .venv,
5) I tried to run: @nsoranzo:matrix.org @hexylena:matrix.org
-bash-4.2$ sh manage_db.sh upgrade
but this fails s:
Activating virtualenv at .venv
Traceback (most recent call last):
File "./scripts/manage_db.py", line 12, in <module>
from galaxy.model.orm.scripts import get_config
File "/home/usern/galaxy/galaxy/lib/galaxy/model/init.py", line 72, in <module>
from sqlalchemy.orm import (
ImportError: cannot import name 'registry'
should I start galaxy and see if the postgres version update happens automatically?
unsure why this upgrade .sh is failing. thoughts? thanks!
./scripts/common_startup.sh before the DB upgrade
Hitting some errors with the postgres initiation/installation following along on the admin training. Using RHEL8:
TASK [galaxyproject.postgresql : Check pgdg repository package (RedHat)] ***************************************************************
fatal: [cpt.agnet.tamu.edu]: FAILED! => {"changed": false, "failures": ["No package pgdg-redhat-repo available."], "msg": "Failed to ins
tall some of the specified packages", "rc": 1, "results": []}
...ignoring
TASK [galaxyproject.postgresql : Install pgdg repository package (RedHat)] *************************************************************
FAILED - RETRYING: Install pgdg repository package (RedHat) (5 retries left).
FAILED - RETRYING: Install pgdg repository package (RedHat) (4 retries left).
FAILED - RETRYING: Install pgdg repository package (RedHat) (3 retries left).
FAILED - RETRYING: Install pgdg repository package (RedHat) (2 retries left).
FAILED - RETRYING: Install pgdg repository package (RedHat) (1 retries left).
fatal: [cpt.agnet.tamu.edu]: FAILED! => {"attempts": 5, "changed": false, "msg": "Failed to validate GPG signature for pgdg-redhat-repo-
42.0-23.noarch"}
PLAY RECAP *****************************************************************************************************************************
cpt.agnet.tamu.edu : ok=9 changed=0 unreachable=0 failed=1 skipped=1 rescued=0 ignored=1I can't quite get this to be bypassed. I've tried some of the modifications here -> ansible/ansible#71634, but to no avail.
Any thoughts on how to fix this?
okay, was able to get past it by successfully implementing the disable_gpg_... setting
However now a new issue with the same thing:
TASK [galaxyproject.postgresql : Install PostgreSQL (RedHat)] **************************************************************************
fatal: [cpt.agnet.tamu.edu]: FAILED! => {"changed": false, "failures": ["postgresql10-server All matches were filtered out by modular fi
ltering for argument: postgresql10-server"], "msg": "Failed to install some of the specified packages", "rc": 1, "results": []}onto the next issue :)
4 replies